Jamming prokaryotic cell-to-cell communications in a model biofilm

Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia

The increased complexity of synthetic microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases in metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics using cell-length control in monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strain's division length, nematic cell alignment in close-packed monolayers can be destabilized. We find that this destabilization confers an emergent, competitive advantage to smaller-length strains-but by mechanisms that differ depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains, and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.

Spatial distribution of mechanical properties in Pseudomonas aeruginosa biofilms, and their potential impacts on biofilm deformation

The mechanical properties of biofilms can be used to predict biofilm deformation under external forces, for example, under fluid flow. We used magnetic tweezers to spatially map the compliance of Pseudomonas aeruginosa biofilms at the microscale, then applied modeling to assess its effects on biofilm deformation. Biofilms were grown in capillary flow cells with Reynolds numbers (Re) ranging from 0.28 to 13.9, bulk dissolved oxygen (DO) concentrations from 1 mg/L to 8 mg/L, and bulk calcium ion (Ca²⁺ ) concentrations of 0 and 100 mg CaCl₂ /L. Higher Re numbers resulted in more uniform biofilm morphologies. The biofilm was stiffer at the center of the flow cell than near the walls. Lower bulk DO led to more stratified biofilms. Higher Ca²⁺ concentrations led to increased stiffness and more uniform mechanical properties. Using the experimental mechanical properties, fluid-structure interaction models predicted up to 64% greater deformation for heterogeneous biofilms, compared with a homogeneous biofilms with the same average properties. However, the deviation depended on the biofilm morphology and flow regime. Our results show significant spatial mechanical variability exists at the microscale, and that this variability can potentially affect biofilm deformation. The average biofilm mechanical properties, provided in many studies, should be used with caution when predicting biofilm deformation.

Molecules Autoinducer 2 and cjA and Their Impact on Gene Expression in

Quorum sensing is a widespread form of cell-to-cell communication, which is based on the production of signaling molecules known as autoinducers (AIs). The first group contains highly species-specific N-acyl homoserine lactones (N-AHLs), generally known as AI-1, which are produced by AHL synthase. The second group, possessing the characteristic structure of a furanone ring, are known as AI-2. The enzyme responsible for their production is S-ribosylhomocysteine lyase (LuxS). In <i>Campylobacter jejuni</i>, AI-2 and LuxS play a role in many important processes, including biofilm formation, stress response, motility, expression of virulence factors, and colonization. However, neither the receptor protein nor the exact structure of the AI-2 molecule have been identified to date. Similarly, little is known about the possible existence of AHL-synthase producing AI-1 and its impact on gene expression. Recently, an analogue of homoserine lactone, called cjA, was isolated from a cell-free supernatant of <i>C. jejuni</i> strain<i></i> 81–176 and from the food isolate c11. The molecule cjA particularly impacted the expression of virulence factors and biofilm formation. This review summarizes the role of AI-2 and cjA in the context of biofilm formation, motility, stress responses, and expression of virulence factors.

Application of 3-D Microfluidic Models for Studying Mass Transport Properties of the Tumor Interstitial Matrix

The physical remodeling associated with cancer progression results in barriers to mass transport in the tumor interstitial space. This hindrance ultimately affects the distribution of macromolecules that govern cell fate and potency of cancer therapies. Therefore, knowing how specific extracellular matrix (ECM) and cellular components regulate transport in the tumor interstitium could lead to matrix normalizing strategies that improve patient outcome. Studies over the past decades have provided quantitative insights into interstitial transport in tumors by characterizing two governing parameters: (1) molecular diffusivity and (2) hydraulic conductivity. However, many of the conventional techniques used to measure these parameters are limited due to their inability to experimentally manipulate the physical and cellular environments of tumors. Here, we examine the application and future opportunities of microfluidic systems for identifying the physiochemical mediators of mass transport in the tumor ECM. Further advancement and adoption of microfluidic systems to quantify tumor transport parameters has potential to bridge basic science with translational research for advancing personalized medicine in oncology.

Microfluidic bioanalytical flow cells for biofilm studies: a review

Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive experimental results include time-varying biofilm properties, structural and chemical heterogeneity, and especially their strong sensitivity to environmental cues. Therefore, in addition to judicious choice of measurement tools, a well-designed biofilm study requires strict control over experimental conditions, more so than most chemical studies. Due to excellent control over a host of physiochemical parameters, microfluidic flow cells have become indispensable in microbiological studies. Not surprisingly, the number of lab-on-chip studies focusing on biofilms and other microbiological systems with expanded analytical capabilities has expanded rapidly in the past decade. In this paper, we comprehensively review the current state of microfluidic bioanalytical research applied to bacterial biofilms and offer a perspective on new approaches that are expected to drive continued advances in this field.

Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems

Bacterial quorum sensing is usually studied in well-mixed populations residing within closed systems. The latter do not exchange mass with their surroundings; however, in their natural environment, such as the rhizosphere, bacteria live in spatially structured open systems. Here, we tested the hypothesis that trapping of bacteria within microscopic pockets of an open system triggers density-dependent differentiation. We designed a microfluidic device that trapped swimming bacteria within microscopic compartments. The geometry of the traps controlled their diffusive coupling to fluid flow that played a dual role as nutrient source and autoinducer sink. Bacillus subtilis differentiates into a state of competence in response to quorum sensing and nutrient limitation. Using a mutant strain with a high differentiation rate and fluorescent reporters for competence, we found that the cell density required for differentiation was 100-fold higher than that required in closed systems. A direct comparison of strongly and moderately coupled reservoirs showed that strong coupling supported early differentiation but required a higher number of bacteria for its initiation. Weak coupling resulted in retardation of growth and differentiation. We conclude that spatial heterogeneity can promote density-dependent differentiation in open systems, and propose that the minimal quorum is determined by diffusive coupling to the environment through a trade-off between retaining autoinducers and accessing nutrients.

Wiring Together Synthetic Bacterial Consortia to Create a Biological Integrated Circuit

The promise of adapting biology to information processing will not be realized until engineered gene circuits, operating in different cell populations, can be wired together to express a predictable function. Here, elementary biological integrated circuits (BICs), consisting of two sets of transmitter and receiver gene circuit modules with embedded memory placed in separate cell populations, were meticulously assembled using live cell lithography and wired together by the mass transport of quorum-sensing (QS) signal molecules to form two isolated communication links (comlinks). The comlink dynamics were tested by broadcasting "clock" pulses of inducers into the networks and measuring the responses of functionally linked fluorescent reporters, and then modeled through simulations that realistically captured the protein production and molecular transport. These results show that the comlinks were isolated and each mimicked aspects of the synchronous, sequential networks used in digital computing. The observations about the flow conditions, derived from numerical simulations, and the biofilm architectures that foster or silence cell-to-cell communications have implications for everything from decontamination of drinking water to bacterial virulence.

Core principles of bacterial autoinducer systems

SUMMARY

Autoinduction (AI), the response to self-produced chemical signals, is widespread in the bacterial world. This process controls vastly different target functions, such as luminescence, nutrient acquisition, and biofilm formation, in different ways and integrates additional environmental and physiological cues. This diversity raises questions about unifying principles that underlie all AI systems. Here, we suggest that such core principles exist. We argue that the general purpose of AI systems is the homeostatic control of costly cooperative behaviors, including, but not limited to, secreted public goods. First, costly behaviors require preassessment of their efficiency by cheaper AI signals, which we encapsulate in a hybrid "push-pull" model. The "push" factors cell density, diffusion, and spatial clustering determine when a behavior becomes effective. The relative importance of each factor depends on each species' individual ecological context and life history. In turn, "pull" factors, often stress cues that reduce the activation threshold, determine the cellular demand for the target behavior. Second, control is homeostatic because AI systems, either themselves or through accessory mechanisms, not only initiate but also maintain the efficiency of target behaviors. Third, AI-controlled behaviors, even seemingly noncooperative ones, are generally cooperative in nature, when interpreted in the appropriate ecological context. The escape of individual cells from biofilms, for example, may be viewed as an altruistic behavior that increases the fitness of the resident population by reducing starvation stress. The framework proposed here helps appropriately categorize AI-controlled behaviors and allows for a deeper understanding of their ecological and evolutionary functions.

Interplay of physical mechanisms and biofilm processes: review of microfluidic methods

Bacteria in natural and artificial environments often reside in self-organized, integrated communities known as biofilms. Biofilms are highly structured entities consisting of bacterial cells embedded in a matrix of self-produced extracellular polymeric substances (EPS). The EPS matrix acts like a biological 'glue' enabling microbes to adhere to and colonize a wide range of surfaces. Once integrated into biofilms, bacterial cells can withstand various forms of stress such as antibiotics, hydrodynamic shear and other environmental challenges. Because of this, biofilms of pathogenic bacteria can be a significant health hazard often leading to recurrent infections. Biofilms can also lead to clogging and material degradation; on the other hand they are an integral part of various environmental processes such as carbon sequestration and nitrogen cycles. There are several determinants of biofilm morphology and dynamics, including the genotypic and phenotypic states of constituent cells and various environmental conditions. Here, we present an overview of the role of relevant physical processes in biofilm formation, including propulsion mechanisms, hydrodynamic effects, and transport of quorum sensing signals. We also provide a survey of microfluidic techniques utilized to unravel the associated physical mechanisms. Further, we discuss the future research areas for exploring new ways to extend the scope of the microfluidic approach in biofilm studies.

Biological noise abatement: coordinating the responses of autonomous bacteria in a synthetic biofilm to a fluctuating environment using a stochastic bistable switch

Noise is inherent to single cell behavior. Its origins can be traced to the stochasticity associated with a few copies of genes and low concentrations of protein and ligands. We have studied the mechanisms by which the response of noisy elements can be entrained for biological signal processing. To elicit predictable biological function, we have engineered a gene environment that incorporates a gene regulatory network with the stringently controlled microenvironment found in a synthetic biofilm. The regulatory network leverages the positive feedback found in quorum-sensing regulatory components of the lux operon, which is used to coordinate cellular responses to environmental fluctuations. Accumulation of the Lux receptor in cells, resulting from autoregulation, confers a rapid response and enhanced sensitivity to the quorum-sensing molecule that is retained after cell division as epigenetic memory. The memory of the system channels stochastic noise into a coordinated response among quorum-sensing signal receivers in a synthetic biofilm in which the noise diminishes with repeated exposure to noisy transmitters on the input of a signaling cascade integrated into the same biofilm. Thus, gene expression in the receivers, which are autonomous and do not communicate with each other, is synchronized to fluctuations in the environment.

Single-cell control of initial spatial structure in biofilm development using laser trapping

Biofilms are sessile communities of microbes that are spatially structured by an embedding matrix. Biofilm infections are notoriously intractable. This arises, in part, from changes in the bacterial phenotype that result from spatial structure. Understanding these interactions requires methods to control the spatial structure of biofilms. We present a method for growing biofilms from initiating cells whose positions are controlled with single-cell precision using laser trapping. The native growth, motility, and surface adhesion of positioned microbes are preserved, as we show for model organisms Pseudomonas aeruginosa and Staphylococcus aureus. We demonstrate that laser-trapping and placing bacteria on surfaces can reveal the effects of spatial structure on bacterial growth in early biofilm development.

Probing cell-cell communication with microfluidic devices

Intercellular communication is a mechanism that regulates critical events during embryogenesis and coordinates signalling within differentiated tissues, such as the nervous and cardiovascular systems. To perform specialized activities, these tissues utilize the rapid exchange of signals among networks that, while are composed of different cell types, are nevertheless functionally coupled. Errors in cellular communication can lead to varied deleterious effects such as degenerative and autoimmune diseases. However, the intercellular communication network is extremely complex in multicellular organisms making isolation of the functional unit and study of basic mechanisms technically challenging. New experimental methods to examine mechanisms of intercellular communication among cultured cells could provide insight into physiological and pathological processes alike. Recent developments in microfluidic technology allow miniaturized and integrated devices to perform intercellular communication experiments on-chip. Microfluidics have many advantages, including the ability to replicate in vitro the chemical, mechanical, and physical cellular microenvironment of tissues with precise spatial and temporal control combined with dynamic characterization, high throughput, scalability and reproducibility. In this Focus article, we highlight some of the recent work and advances in the application of microfluidics to the study of mammalian intercellular communication with particular emphasis on cell contact and soluble factor mediated communication. In addition, we provide some insights into likely direction of the future developments in this field.

Going local: technologies for exploring bacterial microenvironments

Microorganisms lead social lives and use coordinated chemical and physical interactions to establish complex communities. Mechanistic insights into these interactions have revealed that there are remarkably intricate systems for coordinating microbial behaviour, but little is known about how these interactions proceed in the spatially organized communities that are found in nature. This Review describes the technologies available for spatially organizing small microbial communities and the analytical methods for characterizing the chemical environment surrounding these communities. Together, these complementary technologies have provided novel insights into the impact of spatial organization on both microbial behaviour and the development of phenotypic heterogeneity within microbial communities.

Dynamics of AHL mediated quorum sensing under flow and non-flow conditions

Quorum sensing (QS) describes the capability of microbes to communicate with each other by the aid of small molecules. Here we investigate the dynamics of QS-regulated gene expression induced by acylhomoserine lactones (AHLs) in Pseudomonas putida IsoF containing a green fluorescent protein-based AHL reporter. The fluorescence time course of individual colonies is monitored following the external addition of a defined AHL concentration to cells which had previously reached the QS-inactive state in AHL-free medium. Using a microfluidic setup the experiment is performed both under flow and non-flow conditions. We find that without supplying external AHL gene expression is induced without flow while flow suppresses the induction. Both without and with flow, at a low AHL concentration the fluorescence onset is significantly delayed while fluorescence starts to increase directly upon the addition of AHL at a high concentration. The differences between no flow and flow can be accounted for using a two-compartment model. This indicates AHL accumulation in a volume which is not affected by the flow. The experiments furthermore show significant cell-to-cell and colony-to-colony variability which is discussed in the context of a compartmentalized QS mechanism.

Cellular heterogeneity and live cell arrays

In the past decade, the tendency to move from a global, one-size-fits-all treatment philosophy to personalized medicine is based, in part, on the nuanced differences and sub-classifications of disease states. Our knowledge of these varied states stems from not only the ability to diagnose, classify, and perform experiments on cell populations as a whole, but also from new technologies that allow interrogation of cell populations at the individual cell level. Such departures from conventional thinking are driven by the recognition that clonal cell populations have numerous activities that manifest as significant levels of non-genetic heterogeneity. Clonal populations by definition originate from a single genetic origin so are regarded as having a high level of homogeneity as compared to genetically distinct cell populations. However, analysis at the single cell level has revealed a different phenomenon; cells and organisms require an inherent level of non-genetic heterogeneity to function properly, and in some cases, to survive. The growing understanding of this occurrence has lead to the development of methods to monitor, analyze, and better characterize the heterogeneity in cell populations. Following the trend of DNA- and protein microarrays, platforms capable of simultaneously monitoring each cell in a population have been developed. These cellular microarray platforms and other related formats allow for continuous monitoring of single live cells and simultaneously generate individual cell and average population data that are more descriptive and information-rich than traditional bulk methods. These technological advances have helped develop a better understanding of the intricacies associated with biological processes and afforded greater insight into complex biological systems. The associated instruments, techniques, and reagents now allow for highly multiplexed analyses, which enable multiple cellular activities, processes, or pathways to be monitored simultaneously. This critical review will discuss the paradigm shift associated with cellular heterogeneity, speak to the key developments that have lead to our better understanding of systems biology, and detail the future directions of the discipline (281 references).

Imaging in real-time with FRET the redox response of tumorigenic cells to glutathione perturbations in a microscale flow

Despite the potential benefits of selective redox-modulating strategies for cancer therapy, an efficacious methodology for testing therapies remains elusive because of the difficulty in measuring intracellular redox potentials over time. In this report, we have incorporated a new FRET-based biosensor to follow in real time redox-sensitive processes in cells transformed to be tumorigenic and cultured in a microfluidic channel. A microfluidic network was used to control micro-scale flow near the cells and at the same time deliver drugs exogenously. Subsequently, the response of a redox homeostasis circuit was tested, namely reduced glutathione (GSH)/oxidized glutathione(GSSG), to diamide, a thiol oxidant, and two drugs used for cancer therapies: BSO (L-buthionine-[SR]-sulfoximine) and BCNU (carmustine). The main outcome from these experiments is a comparison of the temporal depletion and recovery of GSH in single living cells in real-time. These data demonstrate that mammalian cells are capable of restoring a reduced intracellular redox environment in minutes after an acute oxidative insult is removed. This recovery is significantly delayed by (i) the inhibition of GSH biosynthesis by BSO; (ii) the inactivation of glutathione reductase by BCNU; and (iii) in tumorigenic cells relative to an isogenic non-tumorigenic control cell line.